genomecov
Description
Compute genome-wide coverage statistics. Reports coverage depth across the genome in various output formats.
Example Input
cat example_a.bed
chr1 100 200 gene1 100 +
chr1 150 250 gene2 200 -
chr1 400 500 gene3 300 +
chr2 100 300 gene4 400 +
chr2 500 700 gene5 500 -
cat genome.txt
chr1 1000
chr2 1000
chr3 1000
Command
grit genomecov -i example_a.bed -g genome.txt
Output
chr1 0 750 1000 0.75
chr1 1 200 1000 0.2
chr1 2 50 1000 0.05
chr2 0 600 1000 0.6
chr2 1 400 1000 0.4
chr3 0 1000 1000 1
genome 0 2350 3000 0.783333
genome 1 600 3000 0.2
genome 2 50 3000 0.0166667
Output columns: chromosome, depth, bases at depth, chromosome size, fraction at depth.
Options
| Flag | Description |
|---|---|
-i, --input | Input BED file |
-g, --genome | Genome file (chrom sizes) |
-d, --per-base | Report depth at each position (1-based) |
--bg | Report BedGraph format (non-zero only) |
--bga | Report BedGraph format (including zero coverage) |
--scale | Scale depth by factor (default: 1.0) |
BedGraph Output
Non-zero coverage regions only:
grit genomecov -i example_a.bed -g genome.txt --bg
BedGraph with Zero Coverage
Include zero-coverage regions:
grit genomecov -i example_a.bed -g genome.txt --bga
Per-Base Depth
grit genomecov -i example_a.bed -g genome.txt -d
Scaled Coverage
Apply a scaling factor to depth values:
grit genomecov -i example_a.bed -g genome.txt --scale 0.5
Notes
- Default output is histogram format
- BedGraph formats are useful for genome browsers
- Per-base mode generates large output for whole genomes